Associations between Isolation Source, Clonal Composition, and Antibiotic Resistance Genes in Escherichia coli Collected in Washington State, USA

Mary Jewell; Erica R Fuhrmeister; Marilyn C Roberts; Scott J Weissman; Peter M Rabinowitz; Stephen E Hawes

doi:10.3390/antibiotics13010103

Associations between Isolation Source, Clonal Composition, and Antibiotic Resistance Genes in Escherichia coli Collected in Washington State, USA

Antibiotics (Basel). 2024 Jan 20;13(1):103. doi: 10.3390/antibiotics13010103.

Authors

Mary Jewell¹, Erica R Fuhrmeister^{2

3}, Marilyn C Roberts², Scott J Weissman⁴, Peter M Rabinowitz^{2

5}, Stephen E Hawes¹

Affiliations

¹ Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA 98195, USA.
² Department of Environmental and Occupational Health, School of Public Health, University of Washington, 3980 15th Ave NE, Seattle, WA 98195, USA.
³ Department of Civil and Environmental Engineering, University of Washington, 3760 E. Stevens Way NE, Seattle, WA 98195, USA.
⁴ Division of Infectious Disease, Seattle Children's Hospital, Seattle, WA 98105, USA.
⁵ Center for One Health Research, University of Washington, 3980 15th Ave NE, Seattle, WA 98195, USA.

Abstract

Antimicrobial resistance (AMR) is a global health problem stemming from the use of antibiotics in humans, animals, and the environment. This study used whole-genome sequencing (WGS) of E. coli to explore patterns of AMR across sectors in Washington State, USA (WA). The WGS data from 1449 E. coli isolates were evaluated for isolation source (humans, animals, food, or the environment) and the presence of antibiotic resistance genes (ARGs). We performed sequence typing using PubMLST and used ResFinder to identify ARGs. We categorized isolates as being pan-susceptible, resistant, or multidrug-resistant (MDR), defined as carrying resistance genes for at least three or more antimicrobial drug classes. In total, 60% of isolates were pan-susceptible, while 18% were resistant, and 22% exhibited MDR. The proportion of resistant isolates varied significantly according to the source of the isolates (p < 0.001). The greatest resistance was detected in isolates from humans and then animals, while environmental isolates showed the least resistance. This study demonstrates the feasibility of comparing AMR across various sectors in Washington using WGS and a One Health approach. Such analysis can complement other efforts for AMR surveillance and potentially lead to targeted interventions and monitoring activities to reduce the overall burden of AMR.

Keywords: Escherichia coli; antibiotic resistance; antibiotic resistance genes; whole genome sequencing.

Grants and funding

This research received no external funding.